<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" >
<head>
    <title>Create Epitope</title>

    <style type="text/css">
    html, body {
	    height: 100%;
	    overflow: auto;
    }
    body {
	    padding: 0;
	    margin: 0;
    }
    #silverlightControlHost {
    }
    

	    .style1
        {
            font-size: medium;
        }
</style>
    
    <script type="text/javascript">
<!-- saved from url=(0014)about:internet -->
        
	function ResizeObject( height )
	{ 
	    if (!(height > 0)) {
	        return;
	    }
	//Need both host and slobj to work with both IE and Firefox    
	    var slControl = document.getElementById( "silverlightControl" );
	    slControl.style.height = height + "px";
	    var hostx = document.getElementById( "silverlightControlHost" );
	    hostx.style.height = height; //.ToString() + "px";
	}


        
        function GetVisibleArea()
        {
            return document.documentElement.clientHeight;
        }
    
        function onSilverlightError(sender, args) {
        
            var appSource = "";
            if (sender != null && sender != 0) {
                appSource = sender.getHost().Source;
            } 
            var errorType = args.ErrorType;
            var iErrorCode = args.ErrorCode;
            
            var errMsg = "Unhandled Error in Silverlight 2 Application " +  appSource + "\n" ;

            errMsg += "Code: "+ iErrorCode + "    \n";
            errMsg += "Category: " + errorType + "       \n";
            errMsg += "Message: " + args.ErrorMessage + "     \n";

            if (errorType == "ParserError")
            {
                errMsg += "File: " + args.xamlFile + "     \n";
                errMsg += "Line: " + args.lineNumber + "     \n";
                errMsg += "Position: " + args.charPosition + "     \n";
            }
            else if (errorType == "RuntimeError")
            {           
                if (args.lineNumber != 0)
                {
                    errMsg += "Line: " + args.lineNumber + "     \n";
                    errMsg += "Position: " +  args.charPosition + "     \n";
                }
                errMsg += "MethodName: " + args.methodName + "     \n";
            }

            throw new Error(errMsg);
        }
    </script>
</head>

<body bgcolor="#FFFFCC">
<table border="0" width="100%" cellspacing="0" cellpadding="0">
	<tr>
		<td width="13">&nbsp;</td>
		<td width="511">

		<b>
		<a href="http://research.microsoft.com" style="text-decoration: none">
		<font color="#000000" face="Arial" size="2">Microsoft<br/>
		</font><font face="Arial" size="5" color="#000000">&nbsp;&nbsp;&nbsp; </font>
		<font color="#000000" face="Arial" size="6">Research</font></a></b></td>
		<td width="500">

		<p align="right"><a href="http://research.microsoft.com/research/eScience/" style="text-decoration: none; font-weight: 700"><font size="5" color="#000000" face="Arial">eScience 
		Research Group</font></a></td>
		<td>
		&nbsp;</td>
	</tr>
</table>
<p>
<table border="0" width="100%" cellspacing="0" cellpadding="0">
	<tr>
		<td width="23">&nbsp;</td>
		<td width="1001" bgcolor="#E3E3E1">
		<table border="1" width="100%" bordercolorlight="#D1DBDA" bordercolordark="#FFFFFF" bgcolor="#EEF0ED">
			<tr>
				<td width="265">
		<a href="http://atom.research.microsoft.com/bio/" style="text-decoration: none; font-weight: 700">
				<font color="#666666" size="4" face="Arial">Computational 
				Biology Tools</font></a></td>
				<td>&nbsp;</td>
			</tr>
		</table>
		</td>
		<td>
		&nbsp;</td>
	</tr>
	<tr>
		<td width="23">&nbsp;</td>
		<td width="1001" bgcolor="#E3E3E1">
		<table border="1" width="100%" bordercolorlight="#D1DBDA" bordercolordark="#FFFFFF" bgcolor="#DBDCD7">
			<tr>
				<td width="322"><br>
				<span style="font-weight: 700">
				<font face="Arial" size="6" color="#666666">Create Epitome</font></span></td>
				<td align="left">
				<table border="0" width="278" height="49">
					<tr>
						<td width="91" align="center" valign="bottom"><b>
						<font face="Arial" size="2">
						<a href="Details.htm">
						<font color="#000000">Details</font></a></font></b></td>
						<td width="91" align="center" valign="bottom"><b>
						<font face="Arial" size="2"><a href="#References">
						<font color="#000000">References</font></a></font></b></td>
						<td width="92" align="center" valign="bottom"><b>
						<font face="Arial" size="2"><a href="#Code">
						<font color="#000000">Code</font></a></font></b></td>
					</tr>
				</table>
				</td>
			</tr>
		</table>
		</td>
		<td>
		&nbsp;</td>
	</tr>
	<tr>
		<td width="23" height="532">&nbsp;</td>
		<td width="1001" height="532" bgcolor="#FFFFFF">
		<table border="0" width="1001" height="536">
			<tr>
				<td valign="top"><div id="silverlightControlHost" >
		<font face="Arial">
		<object id="silverlightControl" data="data:application/x-silverlight," type="application/x-silverlight-2" width="800" height="502">
			<param name="source" value="ClientBin/CreateEpitomeSL.xap"/>
			<param name="onerror" value="onSilverlightError" />
			<param name="background" value="white" />
			<param name="minRuntimeVersion" value="2.0.31005.0" />
			<param name="autoUpgrade" value="true" />
			<a href="http://go.microsoft.com/fwlink/?LinkID=124807" style="text-decoration: none;">
     			<img src="http://go.microsoft.com/fwlink/?LinkId=108181" alt="Get Microsoft Silverlight" style="border-style: none"/>
			</a>
		</object>
		<iframe style='visibility:hidden;height:0;width:0;border:0px' name="I1"></iframe>
	</font></div></td>
				<td valign="top">
				<table border="0" width="100%" cellspacing="5" cellpadding="3">
					<tr>
						<td bgcolor="#F2F2F2" valign="top">
						<h2><span class="style1">
						<font face="Arial" size="4" color="#0000FF">About</font></span></h2>
						<p><span class="style1">
						<font size="3" face="Arial" color="#757575">The tool 
						takes amino acid sequences (or text) as input and 
						produces epitomes of all lengths.<br>
&nbsp;</font></span></td>
					</tr>
					<tr>
						<td bgcolor="#F2F2F2" valign="top">
						<h2>



			<span class="style1">
						<font face="Arial" size="4" color="#0000FF">Quick Help</font></span></h2>
						<p><span class="style1">
						<font size="3" face="Arial" color="#757575">Paste (cntl-V) 
						or upload text input text or try a sample.</font></span></p>
						<p><span class="style1">
						<font size="3" face="Arial" color="#757575">Start with 
						&quot;Compute Results&quot; button.</font></span></p>
						<p><span class="style1">
						<font face="Arial" color="#757575" size="3">Select all 
						results (cntl-A)and copy (cntl-C).</font></span></p>
						<p><span class="style1">
						<font size="3" face="Arial" color="#757575">To see 
						all work steps, uncheck the box.<br>
&nbsp;</font></span></td>
					</tr>
				</table>
				</td>
			</tr>
		</table>
		</td>
		<td height="532">
		&nbsp;</td>
	</tr>
	<tr>
		<td width="23">&nbsp;</td>
		<td width="1001" bgcolor="#FFFFFF">



			<span class="style1">
		<table border="0" width="100%" cellspacing="5" cellpadding="5">
			<tr>
				<td width="438" bgcolor="#F2F2F2" valign="top">



			<span class="style1">
				<h2 align="left"><font face="Arial" color="#0000FF" size="4">
				<a name="References">References</a></font></h2>
				<ul>
					<li><font face="Arial" size="3" color="#757575">D. Yerly, D. Heckerman, T. Allen, T. Suscovich, N. Jojic, C. Kadie, W. 
			Pichler, A. Cerny, C. Brander.&nbsp; Design, expression and processing of 
			epitomized HCV encoded CTL epitopes. <i>J. Immunol</i>, to appear.</font></li>
					<li><font color="#757575" face="Arial" size="3">&nbsp;D. Nickle, N. Jojic, D. Heckerman, V. Jojic, D. Kirovski, M. 
			Rolland, S. Pond, J. Mullins. &nbsp;</font></span></span><font face="Arial"><a href="http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0040025">Comparison 
			of immunogen designs that optimize peptide coverage: Reply to 
			Fischer et al.,</a></font><span class="style1"><font color="#757575" face="Arial" size="3"> <i>PLoS Computational Biology</i>, 4(1):e25, 
			January 2008.</font></li>
					<li><font color="#757575" face="Arial" size="3">&nbsp;D. Nickle, M. Rolland, M. Jensen, S. Pond, W. Deng, M. Seligman, 
			D. Heckerman, J. Mullins, and N. Jojic.&nbsp; </font>
			</span>
					<a href="http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030075">
					<font face="Arial">Coping with viral diversity in HIV vaccine design</font></a><span class="style1"><font color="#757575" face="Arial" size="3">, 
					<i>PLoS 
			Computational Biology,</i> 3(4): e75, April 2007.</font></li>
					<li><font color="#757575" face="Arial" size="3">&nbsp;N. Jojic, V. Jojic, B. Frey, C. Meek, and D. Heckerman.&nbsp;
					</font>
			</span>
					<a href="http://books.nips.cc/papers/files/nips18/NIPS2005_0759.pdf">
					<font face="Arial">Using epitomes to model genetic diversity: Rational design of HIV 
			vaccine cocktails</font><font face="Arial" size="3"><span class="style1"><font color="#757575">.</font></span></font></a><span class="style1"><font color="#757575" face="Arial" size="3">&nbsp; NIPS 2005.</font></li>
				</ul></td>
				<td bgcolor="#F2F2F2" valign="top">
				<h2><font face="Arial" size="4" color="#0000FF"><a name="Code">Code</a></font></span></h2>
				<p><span class="style1">
				<font size="3" face="Arial" color="#757575">Downloadable Windows 
				<a href="http://www.codeplex.com/MSCompBio/Wiki/View.aspx?title=Create Epitome&referringTitle=Home">program</a><br>
				Open source 
				<a href="http://www.codeplex.com/MSCompBio/Wiki/View.aspx?title=Create Epitome&referringTitle=Home">code</a>.</font></span></p>
				</td>
			</tr>
		</table>
&nbsp;</td>
		<td>
		<h3><font face="Arial"><br>
&nbsp;</font></h3>
		<p>&nbsp;</td>
	</tr>
</table>
</body>
</html>

<!-- Microsoft Research, eScience Research Group, Microsoft Reciprocal License (Ms-RL)
     Copyright (c) Microsoft Corporation. All rights reserved.
-->